I'm not sure I understand the question, but I'll try to answer. Calibre doesn't replace anything (or remove anything, unless you tell it to) on your reader. The only thing it does is upload any news files that aren't already on your reader onto it. It doesn't sync or anything.

The other night I remember deleting all my old daily news files from my Nook, leave the weekly news files (Businessweek, Times, etc). Then I deleted all news items from my Calibre (including my weekly news items), fetched a newer version of daily news. After plugging and uploading to my Nook, all my weekly news files on my Nook are gone.

So it's like Calibre don't care what news files you are already in your Nook, it will delete them before uploading whatever you have in Calibre.